+Open data
-Basic information
Entry | Database: PDB / ID: 2dq4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of threonine 3-dehydrogenase | ||||||
Components | L-threonine 3-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NAD-DEPENDENT / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information L-threonine 3-dehydrogenase / L-threonine catabolic process to glycine / L-threonine 3-dehydrogenase activity / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Omi, R. / Yao, T. / Goto, M. / Miyahara, I. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of threonine 3-dehydrogenase Authors: Omi, R. / Yao, T. / Goto, M. / Miyahara, I. / Hirotsu, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dq4.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dq4.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 2dq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dq4_validation.pdf.gz | 450.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2dq4_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 2dq4_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 2dq4_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/2dq4 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/2dq4 | HTTPS FTP |
-Related structure data
Related structure data | 2ejvC 1e3jS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36678.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKS4, L-threonine 3-dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.93 Å3/Da / Density % sol: 75.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Sodium Acetate, Mes pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 51941 / % possible obs: 99.8 % / Biso Wilson estimate: 44.6 Å2 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: KETOSE REDUCTASE(ID:1E3J) Resolution: 2.5→19.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2494200.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.0458 Å2 / ksol: 0.337196 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.1 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.99 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
|